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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Binding site similarity measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Binding Sites are compared using Shaper.
For more information, please see the following publication: Desaphy J. et al. Comparison and Druggability Prediction of protein-Ligand Binding sites from pharmacophore-annotated cavity shapes J. Chem. Inf. Model., 2012, 52(8), pp2287-2299
Binding Sites are considered as similar when the similarity value is greater than 0.44

Reference Protein Data Bank Entry :
PDB IDHETUniprot NameEC Number
2xkfBX1Serine/threonine-protein kinase Nek22.7.11.1

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
2xkfBX1Serine/threonine-protein kinase Nek22.7.11.11.000
2xkdT3MSerine/threonine-protein kinase Nek22.7.11.10.602
2xkc4VQSerine/threonine-protein kinase Nek22.7.11.10.601
2xkeWI2Serine/threonine-protein kinase Nek22.7.11.10.595
2xk85R1Serine/threonine-protein kinase Nek22.7.11.10.589
2xk730ESerine/threonine-protein kinase Nek22.7.11.10.584
2wqoVGKSerine/threonine-protein kinase Nek22.7.11.10.583
2z2w770Wee1-like protein kinase2.7.10.20.576
2xk4OL2Serine/threonine-protein kinase Nek22.7.11.10.572
2yac937Serine/threonine-protein kinase PLK12.7.11.210.562
2owb626Serine/threonine-protein kinase PLK12.7.11.210.559
2in6839Wee1-like protein kinase2.7.10.20.555
1x8b824Wee1-like protein kinase2.7.10.20.543
2xnpWCXSerine/threonine-protein kinase Nek22.7.11.10.540
4j531J4Serine/threonine-protein kinase PLK12.7.11.210.532
2xnn430Serine/threonine-protein kinase Nek22.7.11.10.531
2xnmWGZSerine/threonine-protein kinase Nek22.7.11.10.529
2io6330Wee1-like protein kinase2.7.10.20.528
3biz61EWee1-like protein kinase2.7.10.20.528
2xk6EQHSerine/threonine-protein kinase Nek22.7.11.10.527
4i6f1C7Serine/threonine-protein kinase PLK22.7.11.210.526
3cr0809Wee1-like protein kinase2.7.10.20.522
2w5aADPSerine/threonine-protein kinase Nek22.7.11.10.517
4afeGGYSerine/threonine-protein kinase Nek22.7.11.10.517
2xk3XK3Serine/threonine-protein kinase Nek22.7.11.10.514
4j521J3Serine/threonine-protein kinase PLK12.7.11.210.510
4a4o664Serine/threonine-protein kinase PLK12.7.11.210.509
4i6h1C8Serine/threonine-protein kinase PLK22.7.11.210.505
4fk3325Serine/threonine-protein kinase B-raf2.7.11.10.501
3bi6396Wee1-like protein kinase2.7.10.20.499
4f1mACPProbable serine/threonine-protein kinase roco42.7.11.10.492
2ejzSAHDiphthine synthase/0.491
2uagUMAUDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.491
4ftt6HKSerine/threonine-protein kinase Chk12.7.11.10.491
4a4xJUPSerine/threonine-protein kinase Nek22.7.11.10.489
2rkuR78Serine/threonine-protein kinase PLK12.7.11.210.485
2w5bAGSSerine/threonine-protein kinase Nek22.7.11.10.485
3cqeP91Wee1-like protein kinase2.7.10.20.485
3n65XFJNitric oxide synthase, brain1.14.13.390.484
4a4l939Serine/threonine-protein kinase PLK12.7.11.210.482
1t57FMNConserved protein/0.481
2ed3SAHDiphthine synthase/0.481
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.477
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.476
4b6l9ZPSerine/threonine-protein kinase PLK32.7.11.210.472
4twnB96Ephrin type-A receptor 32.7.10.10.469
4bfuZVUPantothenate kinase2.7.1.330.468
2jb4A14Isopenicillin N synthase1.21.3.10.465
5bvw1N1Epithelial discoidin domain-containing receptor 12.7.10.10.465
2y46MIVMycinamicin IV hydroxylase/epoxidase/0.464
2y98MIVMycinamicin IV hydroxylase/epoxidase/0.464
2xnoED8Serine/threonine-protein kinase Nek22.7.11.10.462
4bfxZVXPantothenate kinase2.7.1.330.462
2yvwEPUUDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.461
3wavDWVEctonucleotide pyrophosphatase/phosphodiesterase family member 23.1.4.390.461
1s3uTQDDihydrofolate reductase1.5.1.30.460
2zevB71Geranylgeranyl pyrophosphate synthase/0.460
3n5xXFKNitric oxide synthase, brain1.14.13.390.460
2rjp886A disintegrin and metalloproteinase with thrombospondin motifs 43.4.24.820.459
2a19ANPInterferon-induced, double-stranded RNA-activated protein kinase2.7.11.10.458
2vteIK4UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.458
1ejiTHFSerine hydroxymethyltransferase, cytosolic/0.457
3ctj320Hepatocyte growth factor receptor2.7.10.10.457
4at0FADPossible succinate dehydrogenase/0.457
4qa0SHHHistone deacetylase 83.5.1.980.457
1cqp803Integrin alpha-L/0.455
1uzwCDHIsopenicillin N synthase1.21.3.10.455
2cleF6FTryptophan synthase alpha chain/0.455
2gpjFADSiderophore-interacting protein/0.455
4htx19FcGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.455
3g4iD71cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.454
4bfvZVVPantothenate kinase2.7.1.330.454
4bubADPUDP-N-acetylmuramoyl-L-alanyl-D-glutamate--LD-lysine ligase/0.454
4zirANPEnergy-coupling factor transporter ATP-binding protein EcfA23.6.30.454
4zirANPEnergy-coupling factor transporter ATP-binding protein EcfA1/0.454
5dp2NAPCurF/0.454
1yhjR6CPyridoxal kinase2.7.1.350.452
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.452
2zruFMNIsopentenyl-diphosphate delta-isomerase/0.452
3adaNADSubunit alpha of sarocosine oxidase/0.452
3w1wCHDFerrochelatase, mitochondrial4.99.1.10.452
5uviZMAAdenosine receptor A2a/0.452
1ejbINJ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.451
1xddAAYIntegrin alpha-L/0.451
2gq3COAMalate synthase G/0.451
2uxhQUEHTH-type transcriptional regulator TtgR/0.451
3gncQQQGlutaryl-CoA dehydrogenase/0.451
4bb3KKAIsopenicillin N synthase1.21.3.10.451
4djw0KPBeta-secretase 13.4.23.460.451
1o6qR17Squalene--hopene cyclase4.2.1.1290.450
1t4cCOAFormyl-CoA:oxalate CoA-transferase/0.450
4bfzZVZPantothenate kinase2.7.1.330.450
4gkh0J9Aminoglycoside 3'-phosphotransferase AphA1-IAB/0.450
4heu15JcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.450
3emlZMAAdenosine receptor A2a/0.450
1w06W05Isopenicillin N synthase1.21.3.10.449
2e9aB28Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.449
2vbpVB1Isopenicillin N synthase1.21.3.10.449
4ftq4HKSerine/threonine-protein kinase Chk12.7.11.10.449
2fb8215Serine/threonine-protein kinase B-raf2.7.11.10.448
2iyaZIOOleandomycin glycosyltransferase/0.448
1q5dEPBEpothilone C/D epoxidase1.140.447
2e99B08Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.447
3d3p20AcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.447
1udtVIAcGMP-specific 3',5'-cyclic phosphodiesterase/0.446
3fhxPXLPyridoxal kinase2.7.1.350.446
3prfFP3Serine/threonine-protein kinase B-raf2.7.11.10.446
3qm4PN0Cytochrome P450 2D6/0.446
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
4h3j10WBeta-secretase 13.4.23.460.446
4iarERM5-hydroxytryptamine receptor 1B/0.446
1n8wCOAMalate synthase G/0.445
1pkfEPDEpothilone C/D epoxidase1.140.445
2w6cBM4Acetylcholinesterase3.1.1.70.445
3slkNDPPolyketide synthase extender module 2/0.445
4jbtASDCytochrome P450 monooxygenase/0.445
4r21STRCytochrome P450 family 17 polypeptide 2/0.445
1hfqMOTDihydrofolate reductase1.5.1.30.444
1xomCIOcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.444
3d5wADPSerine/threonine-protein kinase PLK/0.444
1obnASVIsopenicillin N synthase1.21.3.10.443
2g1s4IGRenin3.4.23.150.443
2jn3JN3Fatty acid-binding protein, liver/0.443
2r7b2533-phosphoinositide-dependent protein kinase 12.7.11.10.443
3g4kROLcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.443
4muw2F4cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.443
5iu4ZMAAdenosine receptor A2a/0.443
2jfgUMAUDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.442
2jj2ANPATP synthase subunit beta, mitochondrial3.6.3.140.442
2r0cFADPutative FAD-monooxygenase/0.442
3aw9GDUNAD-dependent epimerase/dehydratase/0.442
4bfwZVWPantothenate kinase2.7.1.330.442
4ddl0JQcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.442
4ft0HK9Serine/threonine-protein kinase Chk12.7.11.10.442
2vd0D27Hematopoietic prostaglandin D synthase/0.441
4bb5HD2Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.441
4fcd0T6cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.441
4isg1FYGlucokinase2.7.1.20.441
1u0wSTLChalcone synthase 22.3.1.740.440
2e07SAHDiphthine synthase/0.440
2e8qSAHDiphthine synthase/0.440
2fgkATPAlpha-hemolysin translocation ATP-binding protein HlyB/0.440
2r6jNDPEugenol synthase 11.1.1.3180.440
2vcmM11Isopenicillin N synthase1.21.3.10.440
3fznD7KBenzoylformate decarboxylase4.1.1.70.440
3h4vDVPPteridine reductase 11.5.1.330.440
3ppkFNISerine/threonine-protein kinase B-raf2.7.11.10.440
3ziaADPATP synthase subunit beta, mitochondrial3.6.3.140.440
3zkyWT4Isopenicillin N synthase1.21.3.10.440
4ea2RWZDehydrosqualene synthase/0.440
4h3f10OBeta-secretase 13.4.23.460.440
5k2cZMAAdenosine receptor A2a/0.440
5k2bZMAAdenosine receptor A2a/0.440